HEADER HYDROLASE 08-NOV-11 4A6P TITLE RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPAIR AND RECOMBINATION PROTEIN RADA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL ATPASE DOMAIN, RESIDUES 108-288 AND 301-349; COMPND 5 SYNONYM: RADA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBAT KEYWDS HYDROLASE, RECOMBINASE EXPDTA X-RAY DIFFRACTION AUTHOR M.E.MARSH,M.T.EHEBAUER,D.SCOTT,C.ABELL,T.L.BLUNDELL,M.HYVONEN REVDAT 4 20-DEC-23 4A6P 1 REMARK REVDAT 3 27-JUL-16 4A6P 1 JRNL REVDAT 2 20-JUL-16 4A6P 1 JRNL REVDAT 1 14-NOV-12 4A6P 0 JRNL AUTH M.E.MARSH,D.E.SCOTT,M.T.EHEBAUER,C.ABELL,T.L.BLUNDELL, JRNL AUTH 2 M.HYVONEN JRNL TITL ATP HALF-SITES IN RADA AND RAD51 RECOMBINASES BIND JRNL TITL 2 NUCLEOTIDES JRNL REF FEBS OPEN BIO V. 6 372 2016 JRNL REFN ESSN 2211-5463 JRNL PMID 27419043 JRNL DOI 10.1002/2211-5463.12052 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 31691 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1623 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 26.5931 - 3.4277 0.94 2804 137 0.1572 0.1623 REMARK 3 2 3.4277 - 2.7215 0.97 2714 169 0.1582 0.2090 REMARK 3 3 2.7215 - 2.3778 0.96 2665 166 0.1699 0.1993 REMARK 3 4 2.3778 - 2.1605 0.88 2478 108 0.1700 0.2166 REMARK 3 5 2.1605 - 2.0057 0.85 2335 142 0.1869 0.2205 REMARK 3 6 2.0057 - 1.8875 0.78 2174 120 0.2210 0.2245 REMARK 3 7 1.8875 - 1.7929 0.93 2560 138 0.1971 0.2190 REMARK 3 8 1.7929 - 1.7149 0.94 2585 135 0.1840 0.2386 REMARK 3 9 1.7149 - 1.6489 0.93 2561 122 0.1829 0.2441 REMARK 3 10 1.6489 - 1.5920 0.94 2604 134 0.1860 0.2259 REMARK 3 11 1.5920 - 1.5422 0.93 2542 139 0.2072 0.2629 REMARK 3 12 1.5422 - 1.4982 0.75 2046 113 0.3619 0.3967 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 37.98 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.30250 REMARK 3 B22 (A**2) : 0.24800 REMARK 3 B33 (A**2) : -1.55050 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1905 REMARK 3 ANGLE : 1.026 2595 REMARK 3 CHIRALITY : 0.069 298 REMARK 3 PLANARITY : 0.004 344 REMARK 3 DIHEDRAL : 15.337 729 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4A6P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1290050152. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32321 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 43.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1PZN REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60 MM NA2HPO4 PH 6.0; 15% PEG 1000, PH REMARK 280 5.8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 30.46000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.61000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.09300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.61000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.46000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.09300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 107 REMARK 465 GLN A 286 REMARK 465 ALA A 287 REMARK 465 ASN A 288 REMARK 465 GLY A 301 REMARK 465 GLY A 302 REMARK 465 HIS A 303 REMARK 465 LYS A 319 REMARK 465 GLY A 320 REMARK 465 PRO A 331 REMARK 465 HIS A 332 REMARK 465 LEU A 333 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2082 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A2090 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH A2093 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A2094 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A2128 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A2136 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A2138 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A2154 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A2189 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A2210 DISTANCE = 7.46 ANGSTROMS REMARK 525 HOH A2211 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A2234 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A2249 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A2250 DISTANCE = 6.69 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1350 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PZN RELATED DB: PDB REMARK 900 RAD51 (RADA) REMARK 999 REMARK 999 SEQUENCE REMARK 999 C TERMINAL DOMAIN RESIDUES 108-349 DBREF 4A6P A 108 349 UNP O74036 RADA_PYRFU 108 349 SEQADV 4A6P MET A 107 UNP O74036 EXPRESSION TAG SEQADV 4A6P ASN A 288 UNP O74036 ARG 288 CLONING ARTIFACT SEQADV 4A6P A UNP O74036 PRO 289 DELETION SEQADV 4A6P A UNP O74036 ASP 290 DELETION SEQADV 4A6P A UNP O74036 ALA 291 DELETION SEQADV 4A6P A UNP O74036 PHE 292 DELETION SEQADV 4A6P A UNP O74036 PHE 293 DELETION SEQADV 4A6P A UNP O74036 GLY 294 DELETION SEQADV 4A6P A UNP O74036 ASP 295 DELETION SEQADV 4A6P A UNP O74036 PRO 296 DELETION SEQADV 4A6P A UNP O74036 THR 297 DELETION SEQADV 4A6P A UNP O74036 ARG 298 DELETION SEQADV 4A6P A UNP O74036 PRO 299 DELETION SEQADV 4A6P A UNP O74036 ILE 300 DELETION SEQRES 1 A 231 MET ALA THR ILE GLY ARG ILE SER THR GLY SER LYS SER SEQRES 2 A 231 LEU ASP LYS LEU LEU GLY GLY GLY ILE GLU THR GLN ALA SEQRES 3 A 231 ILE THR GLU VAL PHE GLY GLU PHE GLY SER GLY LYS THR SEQRES 4 A 231 GLN LEU ALA HIS THR LEU ALA VAL MET VAL GLN LEU PRO SEQRES 5 A 231 PRO GLU GLU GLY GLY LEU ASN GLY SER VAL ILE TRP ILE SEQRES 6 A 231 ASP THR GLU ASN THR PHE ARG PRO GLU ARG ILE ARG GLU SEQRES 7 A 231 ILE ALA GLN ASN ARG GLY LEU ASP PRO ASP GLU VAL LEU SEQRES 8 A 231 LYS HIS ILE TYR VAL ALA ARG ALA PHE ASN SER ASN HIS SEQRES 9 A 231 GLN MET LEU LEU VAL GLN GLN ALA GLU ASP LYS ILE LYS SEQRES 10 A 231 GLU LEU LEU ASN THR ASP ARG PRO VAL LYS LEU LEU ILE SEQRES 11 A 231 VAL ASP SER LEU THR SER HIS PHE ARG SER GLU TYR ILE SEQRES 12 A 231 GLY ARG GLY ALA LEU ALA GLU ARG GLN GLN LYS LEU ALA SEQRES 13 A 231 LYS HIS LEU ALA ASP LEU HIS ARG LEU ALA ASN LEU TYR SEQRES 14 A 231 ASP ILE ALA VAL PHE VAL THR ASN GLN VAL GLN ALA ASN SEQRES 15 A 231 GLY GLY HIS ILE LEU ALA HIS SER ALA THR LEU ARG VAL SEQRES 16 A 231 TYR LEU ARG LYS GLY LYS GLY GLY LYS ARG ILE ALA ARG SEQRES 17 A 231 LEU ILE ASP ALA PRO HIS LEU PRO GLU GLY GLU ALA VAL SEQRES 18 A 231 PHE SER ILE THR GLU LYS GLY ILE GLU ASP HET PO4 A1350 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *432(H2 O) HELIX 1 1 SER A 117 LEU A 124 1 8 HELIX 2 2 GLY A 143 VAL A 155 1 13 HELIX 3 3 PRO A 158 GLY A 162 5 5 HELIX 4 4 ARG A 178 ARG A 189 1 12 HELIX 5 5 ASP A 192 HIS A 199 1 8 HELIX 6 6 ASN A 207 LEU A 226 1 20 HELIX 7 7 THR A 241 TYR A 248 1 8 HELIX 8 8 GLY A 252 ASP A 276 1 25 SHEET 1 AA 2 ARG A 112 ILE A 113 0 SHEET 2 AA 2 ILE A 128 GLU A 129 -1 O ILE A 128 N ILE A 113 SHEET 1 AB 9 ILE A 200 ARG A 204 0 SHEET 2 AB 9 SER A 167 ASP A 172 1 O VAL A 168 N TYR A 201 SHEET 3 AB 9 VAL A 232 ASP A 238 1 N LYS A 233 O SER A 167 SHEET 4 AB 9 ALA A 278 GLN A 284 1 O ALA A 278 N LEU A 235 SHEET 5 AB 9 ALA A 132 GLY A 138 1 O ALA A 132 N VAL A 279 SHEET 6 AB 9 LEU A 311 LYS A 317 1 O LEU A 311 N GLU A 135 SHEET 7 AB 9 LYS A 322 ILE A 328 -1 O ILE A 324 N ARG A 316 SHEET 8 AB 9 ALA A 338 THR A 343 -1 O ALA A 338 N ALA A 325 SHEET 9 AB 9 GLY A 346 GLU A 348 -1 O GLY A 346 N THR A 343 CISPEP 1 ASP A 238 SER A 239 0 5.17 SITE 1 AC1 11 PHE A 140 GLY A 141 SER A 142 GLY A 143 SITE 2 AC1 11 LYS A 144 THR A 145 HOH A2064 HOH A2065 SITE 3 AC1 11 HOH A2071 HOH A2431 HOH A2432 CRYST1 60.920 40.186 87.220 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016415 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024884 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011465 0.00000